COMPARATIVE ANALYSIS OF COMPLETELY SEQUENCED GENOMES

快速增长的数据库完全 细菌、古菌和真核生物的基因组测序 (到1998年底，大约有20个基因组可用， 更多)既创造了新的机会，也创造了新的机会 挑战。为了利用这些信息，我们 开发了一种保守的蛋白质家族系统，包括可能的 来自8个完整的同源蛋白质(直接对应) 测序的基因组。所有公司成立的过程 剩下的完全测序的基因组正在进行中。这 系统允许近乎自动的50%以上的功能注释 在每一个被测试的细菌和古生菌中编码的蛋白质 基因组，尽管只有大约20%的真核蛋白质适合 这些团体。除了功能预测之外，这种方法还 规定了一套系统的古代， 在任何特定情况下缺失的保守蛋白质家族 基因组。对进化模式(即表征)的考察 不同种和系统发育谱系)的科 同源基因表明水平基因转移和 原核生物进化中的谱系特异性基因丢失。更多 具体地说，第一个可用的基因组的比较分析 嗜热菌(Aquifex Aeolicus)与古菌 基因组表明古生菌和古生菌之间存在大量的基因交换 细菌嗜热菌。比较基因组学现在已经成为一种 任何关于特定蛋白质家族或 功能系统。频繁的系统发育检查 结构域和特定结构域蛋白质的分布 架构提供了详细重建的可能性 进化的场景。这样的分析是针对 细菌、古菌和真核生物的DNA修复系统以及 真核细胞程序性死亡系统。的重要作用 水平基因转移和多个结构域的重排 两个系统的演变都得到了演示，并展示了一些新的 并进行了功能预测。

The rapidly growing database of completely sequenced genomes of bacteria, archaea and eukaryotes (approximately 20 genomes available by the end of 1998 and many more in progress) creates both new opportunities and new challenges. In order to take advantage of this information, we developed a system of conserved protein families that include likely orthologous proteins (direct counterparts) from 8 completely sequenced genomes. The process of incorporation of all the remaining completely sequenced genomes is in progress. This system allows nearly automatic functional annotation of more 50% of the proteins encoded in each of the tested bacterial and archaeal genomes, though only about 20% of the eukaryotic proteins fit into these groups. In addition to functional prediction, this approach provides for the systematic delineation of the set of ancient, conserved protein families that are missing in any particular genome. Examination of evolutionary patterns (i.e. representation of different species iand phylogenetic lineages) in the families of orthologs suggests a major role of horizontal gene transfer and lineage specific gene loss in the evolution of prokaryotes. More specifically, comparative analysis of the first available genome of hyperthermophilic bacterium (Aquifex aeolicus) and archaeal genomes indicates massive gene exchange between archaeal and bacterial thermophiles. Comparative genomics has now become a part of any study on the evolution of a particular protein family or a functional system. Frequently examination of the phylogenetic distribution of structural domains and proteins with specific domain architectures provides for the possibility of detailed reconstructions of evolutionary scenarios. Such analyses were performed for the DNA repair systems of bacteria, archaea and eukaryotes and for the eukaryotic programmed cell death systems. Significant roles of horizontal gene transfer and multiple domain rearrangements in the evolution of both systems were demonstrated and a number of new functional predictions were made.